Maria Fyta

Maria Fyta
RWTH Aachen University · Faculty of Mathematics, Computer Science and Natural Sciences

PhD
https://rwth-aachen.de/go/id/suhwq

About

102
Publications
6,675
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1,773
Citations
Additional affiliations
March 2012 - present
University of Stuttgart
September 2008 - February 2012
Technische Universität München
November 2005 - July 2008
Harvard University

Publications

Publications (102)
Article
Room temperature ionic liquid solutions confined between neutral and charged surfaces are investigated by means of atomistic Molecular Dynamics simulations. We study 1-ethyl-3-methylimidazolium dicyanamide ([EMIm]+[DCA]-) in water or dimethylsulfoxide (DMSO) mixtures in confinement between two interfaces. The analysis is based on the comparison of...
Article
Full-text available
A very simple, fast, and efficient approach to analyze and identify respiratory-related virus sequences based on machine learning is proposed. Such schemes are very important in identifying viruses, especially in view of spreading pandemics. The method is based on genetic code rules and the open reading frame (ORF). Data from the respiratory-relate...
Article
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To assess the resilience of energy systems, i.e., the ability to recover after an unexpected shock, the system’s minimum state of service is a key input. Quantitative descriptions of such states are inherently elusive. The measures adopted by governments to contain COVID-19 have provided empirical data, which may serve as a proxy for such states of...
Article
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The interaction of ionic liquids (ILs) with additives or impurities is crucial for the performance of ILs in technological applications. In order to understand the interaction between these, an insight onto the microscopic arrangement of molecules is needed. As a representative case, 1‐ethyl‐3‐methylimidazolium dicyanamide ([EMIM]+[DCA]−) mixtures...
Article
A comprehensive understanding of the interactions between organic molecules and a metal oxide surface is essential for an efficient surface modification and the formation of organic–inorganic hybrids with technological applications ranging from heterogeneous catalysis and biomedical templates up to functional nanoporous matrices. In this work, firs...
Article
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DNA molecules can electrophoretically be driven through a nanoscale opening in a material, giving rise to rich and measurable ionic current blockades. In this work, we train machine learning models on experimental ionic blockade data from DNA nucleotide translocation through 2D pores of different diameters. The aim of the resulting classification i...
Article
The adsorption properties of alkali metal atoms on two dimensional (2D) materials play an important role in the performance of batteries, catalysts, and sensors. In view of designing materials for such applications, we provide a comparative study of the adsorption of alkali metal atoms on different single-layer 2D transition metal dichalcogenides (...
Article
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A modeling approach for atomic‐resolution studies of supported ionic liquid phase (SILP) catalytic systems in silica mesoporous confinement with surface hydroxyl and functional groups is proposed. First, a force field for the Ru‐based catalyst is developed. Second, its solvation behavior within a bulk two‐phase system of heptane and an IL is studie...
Article
The feasibility of synthesizing unnatural DNA/RNA has recently been demonstrated, giving rise to new perspectives and challenges in the emerging field of synthetic biology, DNA data storage, and even the search for extraterrestrial life in the universe. In line with this outstanding potential, solid-state nanopores have been extensively explored as...
Article
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Functionalized nanogaps embedded in nanopores show a strong potential for enhancing the detection of biomolecules. This detection is strongly dependent on the features of the target biomolecules, as well as the characteristics of the sensing device. In this work, through quantum‐ mechanical calculations, we elaborate on representative such aspects...
Article
In view of the wreath of potential functionalities two-dimensional (2D) transition-metal dichalcogenides can offer, we study here tuning pathways of 2D lateral arrangements of structures. Specifically, we have systematically doped a pristine 2D MoS2 with WS2 domains of varying sizes. The resulting materials made of MoS2 with WS2 have distinct struc...
Article
The potential of a two-dimensional (2D) molybdenum-disulfide (MoS2) lateral het- erostructure in sensing small gas molecules is being assessed based on quantum mechan- ical calculations. This heterostructure combines two phases of MoS2, namely a metallic ribbon embedded within the semiconducting MoS2 phase. In this work the influence on the electro...
Article
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DNA units, the nucleobases, are probed with diamond (111) surfaces. The nucleobases are placed on top of a diamond surface interacting in a very specific way with the surface atoms. Different elements, such as hydrogen, nitrogen, and fluorine are chosen for the termination of the diamond. The energetic features and electronic properties of the comb...
Article
We report on the specific interaction of a small diamond‐like molecule, known as dia‐ mondoid, with single amino‐acids forming nano/bio molecular complexes. Using time‐ dependent density‐functional theory calculations we have studied two different relative configurations of three prototypical amino acids, phenylalanine, tyrosine, and tryptophan, wi...
Article
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2D nanopores can be used to electrophoretically drive DNA molecules, which can in turn be identified through measurable electronic current blockades. In this work, we use experimental data from molybdenum disulfide nanopores threading DNA nucleotides and propose a methodological approach to interpret DNA events. Specifically, the experimental ionic...
Article
Electrodes embedded in nanopores have the potential to detect the identity of biomolecules, such as DNA. This identification is typically being done through electronic current measurements across the electrodes in a solvent. In this work, using quantum-mechanical calculations, we qualitatively present the influence of this solvent on the current si...
Article
This work investigates the influence of uncharged interfaces on the distribution of water molecules in three aqueous dialkylimidazolium-based ionic liquid mixtures at various water concentrations. The results are based on atomistic molecular dynamics (MD) simulations supported by sum-frequency generation (SFG) experiments. All outcomes highlight an...
Article
Most of the currently used perovskite-based oxygen-transporting membranes have insufficient resistance towards CO2 and high material costs that potentially limit their commercial applications. In the present work, a highly CO2-tolerant oxygen permeation membrane based on La0.6Ca0.4Co1–xFexO3−δ (x = 0, 0.3, 0.5, 0.7, 1) was designed and prepared by...
Article
DNA mutations and epigenetics have a vital role in the cell development and hu- man diseases. The identification of mutants among healthy nucleotides is indispens- able and engineered nanomaterials can be an ideal platform for the next-generation sequencing technology. Herein, we explore the sensitivity of memantine-thiol diamon- doid, in sensing a...
Article
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Defective nanostructures with a surface termination are the focus of this work. In order to elucidate the influence of the defect on the properties of nanomaterials, we take hydrogen terminated nanodiamonds. Various vacancy defect centers are separately embedded in a nanodiamond at different positions. These include some of the known defects, such...
Article
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Recent experiments demonstrate a highly controlled synthesis of in-plane graphene/hexagonal boron nitride heterostructures, thereby paving the way for the development of a new category of hybrid 2D nanodevices with different interfaces. Herein, by employing a combination of density functional theory (DFT) and the non-equilibrium Green's function fo...
Article
The potential of reading-out DNA molecules using functionalized electrodes embedded in nanopores is discussed here. Focus is given on functionalization using tiny diamond-like hydrogenated cages, the diamondoids. A derivative known as memantine of the smallest diamondoid is taken. This offers hydrogen bonding possibilities. Based on quantum-mechani...
Article
Defect centers such as the negatively charged nitrogen- vacancy defect and the neutral silicon-vacancy and germanium vacancy defect in tiny spherical nanodiamonds are investigated in this work. Quantum mechanical simulations based on density functional theory are performed in order to assess the influence of the surface termination and the defect t...
Article
The characteristics of hybrids made of a defective nanodiamond and a biomolecule unit are investigated in this work. Focus is given on the interaction between the nanodiamond and a DNA nucleobase. The latter is placed close to the former in two different arrangements, realizing different bonding types. The nanodiamond includes a negatively charged...
Article
Copper alloys show a structural variability leading to a range of diverse electronic, transport, and mechanical properties. Here, we investigate the influence of the type and amount of alloying on the electronic transport properties across copper alloys. Specifically, we investigate the electronic transmission along copper in its fcc crystal struct...
Article
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In this work, we present biaxial strain induced modification in the structural and electronic properties of a MoS2 hybrid structure made of a metallic (1T) ribbon embedded in the semiconducting (2H) phase. The results are based on density-functional theory. Biaxial strain is gradually applied on the hybrid structure and the structural modifications...
Article
A coarse-grained model for simulating structural properties of double-stranded RNA is developed with parameters obtained from quantum-mechanical calculations. This model follows a previous parametrization for double-stranded DNA, which is based on mapping the all-atom picture to a coarse-grained four-bead scheme. Chemical and structural differences...
Article
DNA sensing with engineered nanomaterials can bestow a new platform for single nucleotide identification and sequencing. Nevertheless, understanding the relevant nano-bio interfaces can provide a wealth of information on structures, energetics, and dynamics with a great potential in molecular nanotechnology. Herein, we explore the sensitivity of DN...
Article
The rational control of the electronic and optical properties of small functionalized diamond-like molecules, the diamondoids, is the focus of this work. Specifically, we investigate the single- and double- functionalization of the lower diamondoids, adamantane, diamantane, and triamantane with $\mathrm{-NH_2}$ and $\mathrm{-SH}$ groups and extend...
Article
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Using quantum mechanical calculations within the density functional theory, we provide a comprehensive analysis of the infrared-active excitations of water molecules confined within nanocages formed by the beryl crystal lattice. We calculate the infrared-active modes including the translational, librational, and mixed-type resonances of regular and...
Article
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Nanogaps functionalized with small diamond-like particles, diamondoids, have been shown to effectively distinguish between different DNA nucleotides. Here, we focus on the detection of mutations and epigenetic markers using such devices. Based on quantum mechanical simulations within the density functional theory approach coupled with the non-equil...
Article
Full-text available
We develop a theoretical and computational approach to deal with systems that involve a disparate range of spatio-temporal scales, such as those comprised of colloidal particles or polymers moving in a fluidic molecular environment. Our approach is based on a multiscale modeling that combines the slow dynamics of the large particles with the fast d...
Article
We study the properties of residual water molecules at different mole fractions in dialkylimidazolium based ionic liquids (ILs), namely 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIM/BF4) and 1-butyl-3-methylimidazolium tetrafluoroborate (BMIM/BF4) by means of atomistic molecular dynamics (MD) simulations. The corresponding Kirkwood-Buff (KB)...
Article
In this work, we deal with the computational investigation of diamondoid-based molecular conductance junctions and their electronic transport properties. A small diamondoid is placed between the two gold electrodes of the nanogap and is covalently bonded to the gold electrodes through two different molecules, a thiol group and a N-heterocyclic carb...
Article
Molybdenum disulfide (MoS2) is a two-dimensional material in which a semiconducting and a metallic phase can coexist. In this work, we investigate the electronic and transport properties of a hybrid MoS2 monolayer composed of a metallic strip embedded in the semiconducting MoS2 phase. Using quantum mechanical calculations within the density functio...
Article
Small diamond-like particles, diamondoids, have been shown to effectively functionalize gold electrodes in order to sense DNA units passing between the nanopore-embedded electrodes. In this work, we present a comparative study of Au(111) electrodes functionalized with different derivatives of lower diamondoids. Focus is put on the electronic and tr...
Article
The binding energies of complexes of DNA nucleobase pairs are evaluated using quantum mechanical calculations at the level of dispersion corrected density functional theory. We begin with Watson-Crick base pairs of singlets, duplets, and triplets and calculate their binding energies. At a second step, mismatches are incorporated into the Watson-Cri...
Article
Modified tiny hydrogen-terminated diamond structures, known as diamondoids, show a high ef- ficiency in sensing DNA molecules. These diamond cages, as recently proposed, could offer functionalization possibilities for gold junction electrodes. In this investigation, we report on diamondoid-functionalized electrodes, showing that such a device would...
Article
Tiny carbon cages known as diamondoids have recently attracted attention and can be selectively chemically modified. In this work, we focus on lower diamondoids, from adamantane (C10H16) up to (121)-tetramantane ((121)C22H28). Specifically, we investigate a chemical modification based on a member of the carbene family, the imidazolylidene molecule...
Article
N-hetero-cyclic carbenes (NHC)s are emerging as an alternative class of molecules to thiol-based self-assembled monolayers (SAMs), making carbene-based SAMs much more stable in harsh environmental conditions. In this work, we have functionalized tiny diamondoids using NHCs in order to prepare highly stable carbene-mediated diamondoid SAMs on metal...
Book
Computational Approaches in Physics reviews computational schemes which are used in the simulations of physical systems. These range from very accurate ab initio techniques up to coarse-grained and mesoscopic schemes. The choice of the method is based on the desired accuracy and computational efficiency. A bottom-up approach is used to present the...
Article
This review outlines the recent achievements in the field of nanopore research. Nanopores are typically used in single-molecule experiments and are believed to have a high potential to realize an ultra-fast and very cheap genome sequencer. Here, the various types of nanopore materials, ranging from biological to 2D nanopores are discussed together...
Article
Full-text available
Diamondoids are nanoscale diamond-like cage structures with hydrogen terminations, which can occur in various sizes and with a diverse type of modifications. In this work, we focus on the structural alterations and the effect of doping and functionalization on the electronic properties of diamondoids, from the smallest adamantane to heptamantane. T...
Article
Quantum mechanical calculations were used to study the interaction and electronic properties of different DNA units with tiny diamondoids. On p. 3466 F. C. Maier and M. Fyta describe how the relative orientation of the diamondoid and the DNA units plays a significant role in DNA detection.
Article
It has been shown that diamondoids can interact with DNA by forming relatively strong hydrogen bonds to DNA units, such as nucleobases. For this interaction to occur the diamondoids must be chemically modified in order to provide donor/acceptor groups for the hydrogen bond. We show here that the exact arrangement of an amine-modified adamantane wit...
Article
In a recent study we proposed derivatives of lower diamondoids as novel biosensors, as well as possible functionalisation candidates of solid-state nanopores for DNA sequencing. A qualitative analysis has shown the abilities of these molecules to distinguish among different DNA nucleobases. In this letter, we extend the analysis and consider also m...
Article
The possibility of distinguishing between DNA nucleobases of different sizes is manifested here through quantum-mechanical simulations. By using derivatives of small, modified diamond clusters, known as diamondoids, it is possible to separate the pyrimidines (cytosine and thymine) from the larger purines (adenine and guanine), according to the coll...
Article
We predict the stability of diamondoids made up of boron and nitrogen instead of carbon atoms. The results are based on quantum-mechanical calculations within density functional theory (DFT) and show some very distinct features compared to the regular carbon-based diamondoids. These features are evaluated with respect to the energetics and electron...
Article
Understanding the interaction of biological molecules with materials is essential in view of the novel potential applications arising when these two are combined. To this end, we investigate the interaction of DNA with diamondoids, a broad family of tiny hydrogen-terminated diamond clusters with high technological potential. We model this interacti...
Article
Atomistic simulations at two levels, classical and quantum-mechanical, are performed to probe the binding possibilities of the smallest multi-shelled concentric fullerenes, known as “carbon onions”. We focus on the binding behavior of adjacent carbon onions and promote their binding through the addition of vacancies, as well as through doping with...
Article
The electronic structure of diamane, a novel material of ultrathin hydrogenated diamond, is investigated using density-functional-theory based calculations. Focus is given on how defects and dopants can be used to tune the electronic properties of diamane films. We use boron, nitrogen, and sulfur atoms as dopants and focus also on nitrogen-vacancy...
Article
We have developed an efficient multiscale approach to treat biomolecular motion in a fluid solvent. This scheme has been applied to the problem of polymer translocation through a nanopore, an intensively studied subject due to its variety of applications with ultra-fast DNA sequencing being one of them. Our first results involve an anonymous polyme...
Article
Full-text available
We develop force field parameters for the divalent cations Mg(2+), Ca(2+), Sr(2+), and Ba(2+) for molecular dynamics simulations with the simple point charge-extended (SPC/E) water model. We follow an approach introduced recently for the optimization of monovalent ions, based on the simultaneous optimization of single-ion and ion-pair properties. W...
Article
Full-text available
We derive the coarse-grained interactions between DNA nucleotides from ab initio total-energy calculations based on density functional theory (DFT). The interactions take into account base and sequence specificity, and are decomposed into physically distinct contributions that include hydrogen bonding, stacking interactions, backbone, and backbone-...
Article
We employ empirical tight-binding simulations on strained tetrahedral amorphous carbon and diamond nanocomposite networks. For each applied strain, the optoelectronic properties are monitored through the absorption coefficient and the dielectric function. These lead to the optical gaps and are able to quantify the amount of disorder in the structur...
Article
Using molecular dynamics (MD) simulations in conjunction with the SPC/E water model, we optimize ionic force-field parameters for seven different halide and alkali ions, considering a total of eight ion-pairs. Our strategy is based on simultaneous optimizing single-ion and ion-pair properties, i.e., we first fix ion-water parameters based on single...
Article
Results on the structural details of Kirkwood-Buff integrals obtained from the optimization of ionic force fields are presented. We have proposed and make use of an optimization scheme for ionic force fields, which is based on the modification of the cation-anion mixing rules, the calculation of the thermodynamics properties of various monovalent s...
Article
We use computer simulations to study the behavior of amorphous carbon and carbon composites under tensile strain. We investigate the behavior of the optoelectronic properties of these materials as strain is increased. These properties are monitored through the electronic density of states, the optical gap and the Urbach energy for both materials. T...
Article
We propose an optimization scheme to obtain good ionic force fields for classical simulations of salt solutions, also of biological relevance. Our work is based on Molecular Dynamics simulations with explicit (SPC/E) water for different halide and alkali ions forming salt solutions at finite ion concentration. The force field derivation technique w...
Article
The interest in polynucleotide translocation through nanopores has moved from purely biological to the need of realizing nanobiotechnological applications related to personalized genome sequencing. Polynucleotide translocation is a process in which biomolecules, like DNA or RNA, are electrophoretically driven through a narrow pore and their passage...
Article
Full-text available
In this review, we present our recent computational work on carbon-based nanostructured composites. These materials consist of carbon crystallites embedded in an amorphous carbon matrix and are modeled here through classical and semi-empirical quantum-mechanical simulations. We investigate the energetics, mechano-elastic, and optoelectronic propert...
Article
Full-text available
Molecular dynamics simulations of ionic solutions depend sensitively on the force fields employed for the ions. To resolve the fine differences between ions of the same valence and roughly similar size and in particular to correctly describe ion-specific effects, it is clear that accurate force fields are necessary. In the past, optimization strate...
Chapter
Molecular dynamics simulations based on classical force fields have become the standard tool for the modelling of ion specificity in bulk and at interfaces, but the choice of the non-bonding force parameters, the so-called force fields, is a subtle issue. We discuss how thermodynamic solvation properties in the infinite-dilute limit can be used to...
Article
We present a parallel version of MUPHY, a multi-physics/scale code based upon the combination of microscopic Molecular Dynamics (MD) with a hydro-kinetic Lattice Boltzmann (LB) method. The features of the parallel version of MUPHY are hereby demonstrated for the case of translocation of biopolymers through nanometer-sized, multi-pore configurations...
Article
Full-text available
Quantum-mechanical molecular-dynamics simulations are carried out to explore possible precursor states of nano-polycrystalline diamond, a novel ultra-hard material produced directly from graphite. Large-scale simulation with 10^5 atoms is realized by using the ' order-N' simulation code 'ELSES' (http://www.elses.jp). The simulation starts with a di...
Article
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We discuss multiscale simulations of long biopolymer translocation through wide nanopores that can accommodate multiple polymer strands. The simulations provide clear evidence of folding quantization, namely the translocation proceeds through multifolded configurations characterized by a well-defined integer number of folds. As a consequence, the t...
Article
Full-text available
Numerical results on the translocation of long biopolymers through mid-sized and wide pores are presented. The simulations are based on a novel methodology which couples molecular motion to a mesoscopic fluid solvent. Thousands of events of long polymers (up to 8000 monomers) are monitored as they pass through nanopores. Comparison between the diff...
Article
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We investigate the process of biopolymer translocation through a narrow pore using a multiscale approach which explicitly accounts for the hydrodynamic interactions of the molecule with the surrounding solvent. The simulations confirm that the coupling of the correlated molecular motion to hydrodynamics results in significant acceleration of the tr...
Article
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A new multiscale approach for simulating nanobiological flows uses concurrent coupling of constrained molecular dynamics for long biomolecules with a mesoscopic lattice Boltzmann treatment of solvent hydrodynamics. The approach is based on a simple scheme of space- time information exchange between the atomistic and mesoscopic scales.
Article
We present a detailed description of biopolymer translocation through a nanopore in the presence of a solvent, using an innovative multi-scale methodology which treats the biopolymer at the microscopic scale as combined with a self-consistent mesoscopic description for the solvent fluid dynamics. We report evidence for quantized current blockade de...
Article
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The nitrogen-vacancy center in diamond is a promising candidate for realizing the spin qubits concept in quantum information. Even though this defect is known for a long time, its electronic structure and other properties have not yet been explored in detail. We study the properties of the nitrogen-vacancy center in diamond through density function...